The only one I know of is the airbox-to-boot sealing area. There are a few aftermarket kits available to seal this junction better and they're probably money well-spent since an air/dirt leak here will quickly ruin the engine.
Just get some hondabond 4 and seal it from the inside like i did. Mine didn't have any leaks, but i did it as a precautionary measure. The 03 cr250 is a rock solid bike in terms of reliability. As mentioned, just do regular maintenance and enjoy it. The jetting might be a bit finicky like mine was, but a jd jetting kit cured that.